7600638f1611faff7396bd8901b46e79 *DESCRIPTION
eea8c543027706ef42c44d7f2ae9c4c1 *NAMESPACE
e44a6ef146a6df5f2085e810898e1ba3 *NEWS.md
b18f652b239b60c89cd710a1762713dc *R/Baseline.R
df12b5bd4073277a19f475fee9739c07 *R/Core.R
5e9ff3a699566b1b94dddd4b910ea7ca *R/DistToNearest.R
a18848a34df75011eeca7c26167a2cc0 *R/MutationDefinitions.R
3917624d30ecacb6fa6558113699c47a *R/MutationProfiling.R
361f7757cb0cba262541c706ce2ce9f4 *R/RegionDefinitions.R
fc15107719805e91adc25d2798c3756d *R/RegionsExtend.R
9ef955059be0ba4ba913f195e3864e9e *R/Shazam.R
865102bd921dbd0c99a38c8ad734dba8 *R/Shmulate.R
eb9b560edfed22d042ebce0c0cff6477 *R/TargetingModels.R
70059491eea793568ceb871bb52b3eb6 *R/sysdata.rda
e4ac289a5d4753b7f9ca4462eca14fb0 *README.md
20daf777936531ca60401b4338d935ef *build/vignette.rds
4f3f035add5dd931a91adcfba1b27baf *data/CHARGE_MUTATIONS.rda
13597652e61fec4478f242e85d1f3ba5 *data/HH_S1F.rda
a627e8ddc6ef887649482e4f51e39589 *data/HH_S5F.rda
90e5eaa6a08ef93e8b15b32df55c48f8 *data/HKL_S1F.rda
2b74df694e73995d484cec0792f36366 *data/HKL_S5F.rda
31b8bf981c581f80d98fa3cb961b40e4 *data/HYDROPATHY_MUTATIONS.rda
1d29e293a915c4d1f4706535f292329a *data/IMGT_V.rda
4713b40fb5a5c8dbbb3a553576bf8b83 *data/IMGT_VDJ.rda
ee7ff985764d385373f5db509bfcaf1f *data/IMGT_VDJ_BY_REGIONS.rda
16e854af6aabf5ad793aeff99a2608ec *data/IMGT_V_BY_CODONS.rda
deb4ddac9b420d3197189f31c1da30f0 *data/IMGT_V_BY_REGIONS.rda
0c8d4a1f433678c4083485d780fcfe4b *data/IMGT_V_BY_SEGMENTS.rda
914fe6b6ac51d564ef2ba1f85bb85800 *data/MK_RS1NF.rda
c4a1bb3550fd6b5f81a14054add21cb0 *data/MK_RS5NF.rda
6133c0df8fe0735d20445d3c933a2df8 *data/POLARITY_MUTATIONS.rda
ffaafe98d3c5d5c9b31228c6fe6cca47 *data/U5N.rda
e19d67a1cd256df12aea9985917c0683 *data/VOLUME_MUTATIONS.rda
f3b50c606aaca388ab4155ea3428f454 *inst/CITATION
633162ebadeb779b6f07cddccfb087ed *inst/doc/Baseline-Vignette.R
8aca38d942ca9395c133b97353e79eca *inst/doc/Baseline-Vignette.Rmd
3831c09ca0a2ac5ae430f05c5966d8a9 *inst/doc/Baseline-Vignette.pdf
b84e0fb9784ebd2d26ead84cca75f805 *inst/doc/DistToNearest-Vignette.R
cdc995f738b95cac79233505ca34f27e *inst/doc/DistToNearest-Vignette.Rmd
fb58d88a8810adf5d1e5f6c44d1f9e06 *inst/doc/DistToNearest-Vignette.pdf
cd427fd702054a12859598f8376bf2b0 *inst/doc/Mutation-Vignette.R
9339c5d2d2dd916708b5a66117a254b1 *inst/doc/Mutation-Vignette.Rmd
efd5a2aefeb5b40160e6a7abdd2c08d6 *inst/doc/Mutation-Vignette.pdf
b791bd26158541e68c33d0f9851a367b *inst/doc/Shmulate-Vignette.R
55515e374ce9c2dbe893e66c99f362d0 *inst/doc/Shmulate-Vignette.Rmd
480dc48868b65391f053f049cd93eef7 *inst/doc/Shmulate-Vignette.pdf
cc70c81fd5d75b0877d869e3074ba196 *inst/doc/Targeting-Vignette.R
0c85dd613680efeab93432246124c5fc *inst/doc/Targeting-Vignette.Rmd
87e2e5fdb1d5cc36d78b3d77ae9e7065 *inst/doc/Targeting-Vignette.pdf
ce614c872889c5489f8b5e376b1e03d7 *man/Baseline-class.Rd
4c9241edade6d91e3a06f28de4694078 *man/DensityThreshold-class.Rd
b32b0ad8b0c85610fc217a14f1db81b2 *man/GmmThreshold-class.Rd
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223e7522518b67c36b628464b95a52dc *man/HH_S5F.Rd
fd6b00b1452d45467fcf48c64526a794 *man/HKL_S1F.Rd
27710dfa973ae1aa2714463afd1c706a *man/HKL_S5F.Rd
47e947f7796022fe66f6bb95d06aafd1 *man/IMGT_SCHEMES.Rd
52ba6171ad460704b1d9157e9b23b923 *man/MK_RS1NF.Rd
fb4f48c2b4dce0daee89ba3ce5b303cd *man/MK_RS5NF.Rd
830c5c9c1e78673f75a5c297e7c54d11 *man/MUTATION_SCHEMES.Rd
0784db802d5b7527b49cca1214e5343f *man/MutabilityModel-class.Rd
13787752e7a8c6d36e4580366cb8be82 *man/MutationDefinition-class.Rd
b6395c818a08c84df5783fed5ab8c409 *man/RegionDefinition-class.Rd
61f1e2cccdb81bb8a0c0cce1a2480f18 *man/TargetingMatrix-class.Rd
5fb3a8e863923c3423319d03c4ca7da0 *man/TargetingModel-class.Rd
7fb9fdf190107b6241b7b226958c1861 *man/U5N.Rd
77942a00353a374d788ff8cfd45a052f *man/calcBaseline.Rd
c382d48eb26974ccde0459b43aac1f7c *man/calcExpectedMutations.Rd
28671ff2fbb86a8bcc66e1ed52d0cc91 *man/calcObservedMutations.Rd
e360c5f55ef91279e0c90ace525c57d0 *man/calcTargetingDistance.Rd
dcfe2ba5015dd474fbae85b473e81152 *man/calculateMutability.Rd
a10072e80ed50974a97d1f21f091260f *man/collapseClones.Rd
21ad62e80ed159cd868741a625e12323 *man/consensusSequence.Rd
4e0eb86d5e1b4fbf0253f3c292afa783 *man/createBaseline.Rd
de72db904913f5cbcb0a1e6cc145043c *man/createMutabilityMatrix.Rd
291078043a96c53414245a7e245510d4 *man/createMutationDefinition.Rd
492ef3e940bf53f731ef9e5cba3a8653 *man/createRegionDefinition.Rd
7d11f1aee10dede25c1d81cb969fcf9e *man/createSubstitutionMatrix.Rd
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11fb1e7ae75c208a090b94568b9d583e *man/createTargetingModel.Rd
30636a595b9976ec9ea128334344bc2b *man/distToNearest.Rd
0f10a3bd11b7ef8fa9be4fe384d544d1 *man/editBaseline.Rd
fe6d14dde1b8cb3d9a83ad9c57d2ceaf *man/expectedMutations.Rd
d7c9d0bcf61ddb5894afb400b84b8a97 *man/extendMutabilityMatrix.Rd
ad87d67c4a882136c7afa28101a5b37c *man/extendSubstitutionMatrix.Rd
0e2d0715d13b44812842c8e1db911272 *man/findThreshold.Rd
de6352d125ba818a4f31429f1220be1f *man/groupBaseline.Rd
a64599327530e7dd2e26c79dc2bf27ae *man/makeAverage1merMut.Rd
d3ad96cd8466448271e018d0774ebb44 *man/makeAverage1merSub.Rd
a421abd5d1b8546f15e2926a3d3d601d *man/makeDegenerate5merMut.Rd
f1e35fb60180aa5226b1ca07fab136c2 *man/makeDegenerate5merSub.Rd
5fcae87eb1a59f104efe578af61271d4 *man/makeGraphDf.Rd
3b3be58d2c5c40ca58c028f8a51e82e6 *man/minNumMutationsTune.Rd
94699556d289cd6dd2667c60b038662b *man/minNumSeqMutationsTune.Rd
da8d087656261ace366c8b452411d249 *man/observedMutations.Rd
622c0049dc0cc9dbf4eebeca555c151d *man/plotBaselineDensity.Rd
5e2f52216694d5f67f8e7482e24163e8 *man/plotBaselineSummary.Rd
cf65429261fc48ae7b596ea422238d63 *man/plotDensityThreshold.Rd
767b693dd2766bce94522103c3bb3459 *man/plotGmmThreshold.Rd
dd51d0355510732690a33bea5186ace5 *man/plotMutability.Rd
17095b8bfb1217af965e15a469bf7888 *man/plotTune.Rd
4d11abe48d8f5e735225cea8bc6de2f4 *man/setRegionBoundaries.Rd
e946ccbbd09fe107e00855ce1e8746f5 *man/shazam.Rd
ab6c72f099c6fac7cb2c127428f58e16 *man/shmulateSeq.Rd
1b69477030e9204221b91d6e138f2259 *man/shmulateTree.Rd
7ff7bbe22f652c8ea5ed2c6f752a7638 *man/slideWindowDb.Rd
9ee27a125bda5fd7a296641495d9de29 *man/slideWindowSeq.Rd
3644a691b5aece662d8920745f91c298 *man/slideWindowTune.Rd
0a6e9a63813d58f2383d52fe98230a0b *man/slideWindowTunePlot.Rd
820146be6dfcfe9b6f29bac411d48ba4 *man/summarizeBaseline.Rd
a347b3e7a51961a499586a701b9921f2 *man/testBaseline.Rd
eb562fee7fda5169a426ea340a6a0dc3 *man/writeTargetingDistance.Rd
8aca38d942ca9395c133b97353e79eca *vignettes/Baseline-Vignette.Rmd
cdc995f738b95cac79233505ca34f27e *vignettes/DistToNearest-Vignette.Rmd
9339c5d2d2dd916708b5a66117a254b1 *vignettes/Mutation-Vignette.Rmd
55515e374ce9c2dbe893e66c99f362d0 *vignettes/Shmulate-Vignette.Rmd
419916bac0eb8cec6ad6a664476d48f4 *vignettes/Shmulate-Vignette.html
0c85dd613680efeab93432246124c5fc *vignettes/Targeting-Vignette.Rmd
